1O75

Tp47, the 47-Kilodalton Lipoprotein of Treponema pallidum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the 47-kDa Lipoprotein of Treponema Pallidum Reveals a Novel Penicillin-Binding Protein

Deka, R.K.Machius, M.Norgard, M.V.Tomchick, D.R.

(2002) J.Biol.Chem. 277: 41857

  • DOI: 10.1074/jbc.M207402200

  • PubMed Abstract: 
  • Syphilis is a complex sexually transmitted disease caused by the spirochetal bacterium Treponema pallidum. T. pallidum has remained exquisitely sensitive to penicillin, but the mode of action and lethal targets for beta-lactams are still unknown. We ...

    Syphilis is a complex sexually transmitted disease caused by the spirochetal bacterium Treponema pallidum. T. pallidum has remained exquisitely sensitive to penicillin, but the mode of action and lethal targets for beta-lactams are still unknown. We previously identified the T. pallidum 47-kDa lipoprotein (Tp47) as a penicillin-binding protein (PBP). Tp47 contains three hypothetical consensus motifs (SVTK, TEN, and KTG) that typically form the active center of other PBPs. Yet, in this study, mutations of key amino acids within these motifs failed to abolish the penicillin binding activity of Tp47. The crystal structure of Tp47 at a resolution of 1.95 A revealed a fold different from any other known PBP; Tp47 is predominantly beta-sheet, in contrast to the alpha/beta-fold common to other PBPs. It comprises four distinct domains: two complex beta-sheet-containing N-terminal domains and two C-terminal domains that adopt immunoglobulin-like folds. The three hypothetical PBP signature motifs do not come together to form a typical PBP active site. Furthermore, Tp47 is unusual in that it displays beta-lactamase activity (k(cat) for penicillin = 271 +/- 6 s(-1)), a feature that hindered attempts to identify the active site in Tp47 by co-crystallization and mass spectrometric techniques. Taken together, Tp47 does not fit the classical structural and mechanistic paradigms for PBPs, and thus Tp47 appears to represent a new class of PBP.


    Related Citations: 
    • The 47-kDa Major Lipoprotein Immunogen of Treponema Pallidum is a Penicillin-Binding Protein with Carboxypeptidase Activity
      Weigel, L.M.,Radolf, J.D.,Norgard, M.V.
      (1994) Proc.Natl.Acad.Sci. USA 91: 11611


    Organizational Affiliation

    Departments of Microbiology and Biochemistry, University of Texas Southwestern Medical Center, Dallas 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
47 KDA MEMBRANE ANTIGEN
A, B
415Treponema pallidum (strain Nichols)N/A
Find proteins for P29723 (Treponema pallidum (strain Nichols))
Go to UniProtKB:  P29723
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PDX
Query on PDX

Download SDF File 
Download CCD File 
A, B
2,3-DI-O-SULFO-ALPHA-D-GLUCOPYRANOSE
C6 H12 O12 S2
ORUZACWROKWTRH-DVKNGEFBSA-N
 Ligand Interaction
XE
Query on XE

Download SDF File 
Download CCD File 
A, B
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.931α = 90.00
b = 128.931β = 90.00
c = 151.161γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MLPHAREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance